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GSTM1 in complex with GSH and bithionol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M Amino acids, 0.1 M MES pH 6.0 - 7.0, 40%-50% Mix1(Mix1: 40% v/v PEG550*MME, 20% w/v PEG20000)
Crystal Properties Matthews coefficient Solvent content 2.68 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.129 α = 90 b = 83.799 β = 90 c = 213.008 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2022-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9792 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.15 50.01 98.7 0.12 0.039 0.337 13 8.6 55890
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 95.4 0.337 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6a38 2.15 41.93 53015 2827 98.61 0.2295 0.22818 0.2336 0.2541 0.2618 RANDOM 50.164
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.31 -0.4 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.482 r_long_range_B_refined 6.313 r_long_range_B_other 6.277 r_dihedral_angle_1_deg 5.611 r_dihedral_angle_2_deg 5.452 r_scangle_other 2.18 r_mcangle_it 2.03 r_mcangle_other 2.03 r_scbond_it 1.281 r_scbond_other 1.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.482 r_long_range_B_refined 6.313 r_long_range_B_other 6.277 r_dihedral_angle_1_deg 5.611 r_dihedral_angle_2_deg 5.452 r_scangle_other 2.18 r_mcangle_it 2.03 r_mcangle_other 2.03 r_scbond_it 1.281 r_scbond_other 1.281 r_mcbond_it 1.15 r_mcbond_other 1.15 r_angle_refined_deg 0.976 r_angle_other_deg 0.368 r_chiral_restr 0.054 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7248 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction xia2 data reduction MOLREP phasing